Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate WP_057507154.1 ABB28_RS02775 aldo/keto reductase
Query= BRENDA::F2YCN5 (340 letters) >NCBI__GCF_001431535.1:WP_057507154.1 Length = 318 Score = 117 bits (294), Expect = 3e-31 Identities = 90/306 (29%), Positives = 150/306 (49%), Gaps = 31/306 (10%) Query: 32 AIGGWMWG-GTDDDASIKTIHRAIDLGINIIDTAPAYGR-------GHAEEVVGK--AIK 81 A GG ++G D+ + + +D G N++DTA AY G +E ++G+ A Sbjct: 18 AFGGNVFGWSADEKTTFALLDAFVDAGFNLVDTADAYSAWVPGNQGGESETLIGRWFARS 77 Query: 82 GQRDNLIIATKVGLDWTLTPDQSMRRNSSASRIKKEIEDSLRRLGTDYIDLYQVHWPDPL 141 G+RD +++ATKV W+ P SA I +E SLRRL TD IDLYQ H D Sbjct: 78 GKRDKVVLATKVA-KWSEQP------GLSADNITAAVEGSLRRLQTDVIDLYQAHEDDES 130 Query: 142 VPIEETATILEALRKEGKIRSIGVSNYSVQQM-DEFKKYAELAVS-----QSPYNLFERE 195 P+E T L ++GK+R+IG SN+S +++ D K A+ + Q YNL++R Sbjct: 131 TPLETTLGAFARLIEQGKVRAIGASNFSAERLADALKVSADYQLPRYETLQPEYNLYDRS 190 Query: 196 -IDKDILPYAKKNDLVVLGYGALCRGLLSG--RMTADRAFTGDDLRKTDPKFQKPRFEHY 252 + + ++ L V+ Y +L G LSG R T D + + + K+ PR Sbjct: 191 GYEAGLEALVQREQLGVISYYSLASGFLSGKYRRTEDASRSPARGQSVVAKYLNPRGNRI 250 Query: 253 LAAVEELKKLAKEHYNKSVLALAIRWMLEQ-GPTLALWGACKPEQIDGIDEVFGWQISDE 311 LAA++++ + + +A+ W++ + T + A EQ+ + +S + Sbjct: 251 LAALDDV----ASRHTATASQVALAWLIARPSITAPIVSATSVEQLHDVLAAATLALSAQ 306 Query: 312 DLKQID 317 D+ ++D Sbjct: 307 DIAELD 312 Lambda K H 0.317 0.136 0.407 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 258 Number of extensions: 9 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 340 Length of database: 318 Length adjustment: 28 Effective length of query: 312 Effective length of database: 290 Effective search space: 90480 Effective search space used: 90480 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory